Changeset 3531


Ignore:
Timestamp:
Jun 26, 2007, 1:12:48 PM (14 years ago)
Author:
Martin Svensson
Message:

References #358. Some changes on the log statements

Location:
trunk/src/clients/migrate/net/sf/basedb/clients/migrate
Files:
35 edited

Legend:

Unmodified
Added
Removed
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/AnnotationTransfer.java

    r3529 r3531  
    7272      AnnotationTypeTransfer annotationTypeT)
    7373  {
     74    log.debug("Checking that necessary transfers have been done before proceeding with Annotations");
    7475    if (sampleT.isDone() && annotationTypeT.isDone())
    7576    {
     
    153154          // Annotations with invalid data are not migrated
    154155          log.error("Annotation: " + annotation + " has invalid data and is not migrated");
    155           if (log.isDebugEnabled()) log.debug(e);
     156          if (log.isDebugEnabled()) log.debug("\t" + e);
    156157        }
    157158        catch (NumberFormatException e)
     
    159160          // Annotations with invalid data are not migrated
    160161          log.error("Annotation: " + annotation + " has a number with invalid format and is not migrated");
    161           if (log.isDebugEnabled()) log.debug(e);
     162          if (log.isDebugEnabled()) log.debug("\t" + e);
    162163        }
    163164      }
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/AnnotationTypeTransfer.java

    r3529 r3531  
    6565  {
    6666    super(userT, groupT);
     67    log.debug("Checking that necessary transfers have been done before proceeding with AnnotationTypes");
    6768    if (!userT.isDone() || !groupT.isDone())
    6869    {
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArrayBlockTransfer.java

    r3529 r3531  
    7575      MappedPlateTransfer mappedPlateT, ReporterTransfer reporterT)
    7676  {
     77    log.debug("Checking that necessary transfers have been done before proceeding with ArrayBlocks");
    7778    if (arrayTypeT != null && arrayTypeT.isDone() && mappedPlateT != null
    7879        && mappedPlateT.isDone() && reporterT != null
     
    254255          {
    255256            log.warn("Couldn't get feature data");
    256             if (log.isDebugEnabled())log.debug(e);
     257            if (log.isDebugEnabled()) log.debug("\t" + e);
    257258          }
    258259        }
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArraySlideTransfer.java

    r3529 r3531  
    7272  {
    7373    super(userT, groupT);
     74    log.debug("Checking that necessary transfers have been done before proceeding with ArraySlides");
    7475    if (arrayBatchT != null && arrayBatchT.isDone())
    7576    {
     
    155156    {
    156157      log.warn("Couldn't get array slide with id: " + slideId + " from BASE1");
    157       if (log.isDebugEnabled()) log.debug(e);
     158      if (log.isDebugEnabled()) log.debug("\t" + e);
    158159    }
    159160    return null;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArrayTypePlateTransfer.java

    r3529 r3531  
    6969  ArrayTypePlateTransfer(ArrayTypeTransfer arrayTypeT, MappedPlateTransfer plateT)
    7070  {
     71    log.debug("Checking that necessary transfers have been done before proceeding with ArrayTypePlate");
    7172    if (arrayTypeT != null && arrayTypeT.isDone())
    7273    {
     
    127128    {
    128129      log.warn("Couldn't get plate list");
    129       if (log.isDebugEnabled())log.debug(e);
     130      if (log.isDebugEnabled())log.debug("\t" + e);
    130131    }
    131132    return plates;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ArrayTypeTransfer.java

    r3529 r3531  
    127127    {
    128128      log.warn("Couldn't get ArrayDesign by id: '" + base1ArrayDesignId + "' in BASE1");
    129       if (log.isDebugEnabled())log.debug(e);
     129      if (log.isDebugEnabled())log.debug("\t" + e);
    130130    }
    131131    return null;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ExperimentTransfer.java

    r3529 r3531  
    7272  {
    7373    super(userT, groupT);
     74    log.debug("Checking that necessary transfers have been done before proceeding with Experiment");
    7475    if (rbaT != null && rbaT.isDone())
    7576    {
     
    110111    if (log.isDebugEnabled())
    111112    {
    112       log.debug("...transfers Experiment with id:" + rs.getInt(1) + " from BASE1");
     113      log.debug("Transfers Experiment:" + rs.getString(6) + " with id:" + rs.getInt(1) + " from BASE1");
    113114    }
    114115    Experiment experiment = Experiment.getNew(
     
    130131      experiment.setPublicationDate(null);
    131132      log.warn("PublicationDate couldn't be set for this Experiment");
    132       if (log.isDebugEnabled())log.debug(e);
     133      if (log.isDebugEnabled())log.debug("\t" + e);
    133134    }
    134135    addRawBioAssays(dc, experiment, rs.getInt(1));
     
    160161            if (log.isDebugEnabled())
    161162            {
    162               log.debug("...RawBioAssay:" + rba.getName() + " added to Experiment:" + experiment.getName());
     163              log.debug("RawBioAssay:" + rba.getName() + " added to Experiment:" + experiment.getName());
    163164            }
    164165          }
     
    166167          {
    167168            log.warn("Couldn't add RawBioAssay:" + rba.getName() + " to Experiment:" + experiment.getName());
    168             if (log.isDebugEnabled())log.debug(e);
     169            if (log.isDebugEnabled())log.debug("\t" + e);
    169170          }
    170171        }
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ExtractTransfer.java

    r3529 r3531  
    6666  {
    6767    super(userT, groupT, protocolT);
     68    log.debug("Checking that necessary transfers have been done before proceeding with Extract");
    6869    this.sampleT = sampleT;
    6970    if (!sampleT.isDone())
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/FileTransfer.java

    r3529 r3531  
    239239      if (log.isDebugEnabled())
    240240      {
    241         log.debug(e);
     241        log.debug("\t" + e);
    242242      }
    243243    }
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/GroupTransfer.java

    r3529 r3531  
    7171  GroupTransfer(UserTransfer userT, QuotaTransfer quotaT)
    7272  {
     73    log.debug("Checking that necessary transfers have been done before proceeding with Groups");
    7374    if (userT.isDone() && quotaT.isDone())
    7475    {
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/HardwareTransfer.java

    r3529 r3531  
    126126    {
    127127      log.warn("Couldn't get hardware in BASE1 by id: " + base1HardwareId);
    128       if(log.isDebugEnabled()) log.debug(e);
     128      if(log.isDebugEnabled()) log.debug("\t" + e);
    129129    }
    130130    return null;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/HybridizationTransfer.java

    r3529 r3531  
    7878  {
    7979    super(userT, groupT);
     80    log.debug("Checking that necessary transfers have been done before proceeding with Hybridization");
    8081    if (arraySlideT.isDone() && labeledExtractT.isDone() && protocolT.isDone())
    8182    {
     
    118119      throws BaseException, SQLException
    119120  {   
     121    log.debug("transfer Hybridization:" + rs.getInt(6) + " with id " + rs.getInt(1) + " from BASE1");
    120122    Hybridization hybridization = Hybridization.getNew(dc);
    121123    setCommonItemData(dc, (CommonItem) hybridization, rs);
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ImageFileTransfer.java

    r3529 r3531  
    7777  {
    7878    super(userT, groupT);
     79    log.debug("Checking that necessary transfers have been done before proceeding with ImageFile");
    7980    if (scanT != null && scanT.isDone() && uploadFT != null
    8081        && uploadFT.isDone())
     
    175176    {
    176177      log.warn("Couldn't get Image with id: " + base1ImageId + " from BASE1");
    177       if (log.isDebugEnabled())log.debug(e);
     178      if (log.isDebugEnabled())log.debug("\t" + e);
    178179    }
    179180    return null;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/LabeledExtractTransfer.java

    r3529 r3531  
    7575  {
    7676    super(userT, groupT, protocolT);
     77    log.debug("Checking that necessary transfers have been done before proceeding with LabeledExtract");
    7778    if (extractT.isDone() && labelT.isDone())
    7879    {
     
    159160      if (log.isDebugEnabled())
    160161      {
    161         log.debug(e);
     162        log.debug("\t" + e);
    162163      }
    163164    }
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/MappedPlateTransfer.java

    r3529 r3531  
    9797  {
    9898    super(userT, groupT);
     99    log.debug("Checking that necessary transfers have been done before proceeding with MappedPlate");
    99100    if (reporterT.isDone() && unmappedPlateT.isDone())
    100101    {
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/MeasuredBioMaterialTransfer.java

    r3529 r3531  
    6969  {
    7070    super(userT, groupT);
     71    log.debug("Checking that necessary transfers have been done before proceeding with MeasuredBioMaterials");
    7172    this.protocolT = protocolT;
    7273    if (!protocolT.isDone())
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/PlateEventTransfer.java

    r3529 r3531  
    6666      PlateEventTypeTransfer plateEventTypeT, ProtocolTransfer protocolT)
    6767  {
     68    log.debug("Checking that necessary transfers have been done before proceeding with PlateEvent");
    6869    if (mappedPlateT.isDone() && plateEventTypeT.isDone()
    6970        && protocolT.isDone())
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/PlateEventTypeTransfer.java

    r3529 r3531  
    6565      PlateTypeTransfer plateTypeT)
    6666  {
     67    log.debug("Checking that necessary transfers have been done before proceeding with PlateEventType");
    6768    if (protocolTypeT.isDone() && plateTypeT.isDone())
    6869    {
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/PlateTypeTransfer.java

    r3529 r3531  
    138138    {
    139139      log.warn("Couldn't get plate by id " + base1PlateTypeId + "from BASE1");
    140       if (log.isDebugEnabled()) log.debug(e);
     140      if (log.isDebugEnabled()) log.debug("\t" + e);
    141141    }
    142142    return null;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/PluginTransfer.java

    r3529 r3531  
    180180    {
    181181      log.warn("Couldn't create configuration file for BASE 1 plugin");
     182      if (log.isDebugEnabled()) log.debug("\t" + e);
    182183    }
    183184    catch (SQLException e)
     
    250251    {
    251252      log.warn("Couldn't create plugin definition of Base1PluginExecuter", e);
     253      if (log.isDebugEnabled()) log.debug("\t" + e);
    252254    }
    253255    return pluginDefinition;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ProtocolTransfer.java

    r3529 r3531  
    6868  {
    6969    super(userT, groupT);
     70    log.debug("Checking that necessary transfers have been done before proceeding with Protocol");
    7071    if (protocolTypeT.isDone())
    7172    {
     
    175176      if (log.isDebugEnabled())
    176177      {
    177         log.debug(e);
     178        log.debug("\t" + e);
    178179      }
    179180    }
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ProtocolTypeTransfer.java

    r3529 r3531  
    138138    {
    139139      log.warn("FAILED when getting protocol type by ID");
    140       if (log.isDebugEnabled()) log.debug(e);
     140      if (log.isDebugEnabled()) log.debug("\t" + e);
    141141    }
    142142    return null;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayDataTransfer.java

    r3529 r3531  
    7979  {
    8080    super(userT, groupT);
     81    log.debug("Checking that necessary transfers have been done before proceeding with RawBioAssayData");
    8182    if (rbaT != null && rbaT.isDone() && arrayTypeT != null
    8283        && arrayTypeT.isDone() && reporterT != null
     
    260261      if (log.isDebugEnabled())
    261262      {
    262         log.debug("...transfered " + rowCount + " rows of RawData");
     263        log.debug("transfered " + rowCount + " rows of RawData");
    263264      }
    264265    }
     
    271272    {
    272273      log.warn("Couldn't get RawData from BASE1");
    273       log.debug(e);
     274      log.debug("\t" + e);
    274275      progress.increase();
    275276    }
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayTransfer.java

    r3529 r3531  
    7272  {
    7373    super(userT, groupT);
     74    log.debug("Checking that necessary transfers have been done before proceeding with RawBioAssay");
    7475    if (uploadFT != null && uploadFT.isDone() && scanT != null
    7576        && scanT.isDone() && arrayTypeT != null && arrayTypeT.isDone())
     
    115116      throws BaseException, SQLException
    116117  {
    117     if (log.isDebugEnabled()) log.debug("Starts to transfer RawBioAssay with BASE1 id:" + rs.getInt(1));
     118    if (log.isDebugEnabled()) log.debug("transfer RawBioAssay with id:" + rs.getInt(1) + " from  BASE1");
    118119    RawBioAssay rawBioAssay = RawBioAssay.getNew(
    119120        dc, RawDataTypes.getRawDataType("genepix"));
     
    201202    {
    202203      log.warn("Couldn't get RawBioAssay with BASE1 id: " + base1Id);
    203       if (log.isDebugEnabled()) log.debug(e);
     204      if (log.isDebugEnabled()) log.debug("\t" + e);
    204205    }
    205206    return null;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ReporterTransfer.java

    r3529 r3531  
    154154        if (log.isDebugEnabled())
    155155        {
    156           log.debug("Transfered reporter: " + item.getName() + " successfully");
     156          log.debug("Transfered reporter: " + item.getExternalId() + " successfully");
    157157          log.debug("--------------------------------------------------------------------------");
    158158        }
     
    161161      {
    162162        // Fetch next batch
     163        log.debug("fetching next batch");
    163164        run(ps, from + size, size);
    164165      }
     
    197198        if (log.isDebugEnabled())
    198199        {
    199           log.debug("Reporter: " + reporter.getName() + " has been mapped");
     200          log.debug("Reporter: " + reporter.getExternalId() + " has been mapped");
    200201        }
    201202      }
     
    231232    if (log.isDebugEnabled())
    232233    {
    233       log.debug("Transfering Reporter BASE1 id(" + rs.getInt(1) + ")\tBASE1 reporterId(" + externalId + ")");
     234      log.debug("Transfering Reporter BASE1 id(" + rs.getInt(1) + ")\texternal Id(" + externalId + ")");
    234235    }
    235236    externalIdMap.put(externalId, rs.getInt(1));
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/SampleTransfer.java

    r3529 r3531  
    6969  SampleTransfer(UserTransfer userT, GroupTransfer groupT,
    7070      ProtocolTransfer protocolFT, SampleTissueTransfer sampleTissueT)
    71   {
     71  {   
    7272    super(userT, groupT, protocolFT);
     73    log.debug("Checking that necessary transfers have been done before proceeding with Samples");
    7374    if (sampleTissueT.isDone())
    7475    {
     
    166167    {
    167168      log.warn("Couldn't get sample in BASE1 by id: " + base1SampleId);
    168       if (log.isDebugEnabled()) log.debug(e);
     169      if (log.isDebugEnabled()) log.debug("\t" + e);
    169170    }
    170171    return null;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/ScanTransfer.java

    r3529 r3531  
    6060  {
    6161    super(userT, groupT);
     62    log.debug("Checking that necessary transfers have been done before proceeding with Scan");
    6263    if (hybridizationT.isDone() && hardwareT.isDone())
    6364    {
     
    113114      {
    114115        log.debug("Transfered Scan: " + scan.getName() + "\tBASE1 id(" + rs.getInt(1) + ")");
     116        log.debug("--------------------------------------------------------------------------");
    115117      }
    116118      return scan;
     
    137139    {
    138140      log.warn("Couldn't get Scan with id " + base1ScanId + " in BASE1");
    139       if (log.isDebugEnabled()) log.debug(e);
     141      if (log.isDebugEnabled()) log.debug("\t" + e);
    140142    }
    141143    return null;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/SharedItemTransfer.java

    r3529 r3531  
    8383  SharedItemTransfer(UserTransfer userT, GroupTransfer groupT)
    8484  {
     85    log.debug("Checking that necessary transfers have been done before proceeding with SharedItems");
    8586    if (userT.isDone() && groupT.isDone())
    8687    {
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/SoftwareTransfer.java

    r3529 r3531  
    110110    {
    111111      log.warn("Couldn't get software in BASE1 by id: " + base1SoftwareId);
    112       if (log.isDebugEnabled()) log.debug(e);
     112      if (log.isDebugEnabled()) log.debug("\t" + e);
    113113    }
    114114    return null;
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/Transfer.java

    r3529 r3531  
    472472      {
    473473        log.warn("Item already exists " + id);
    474         if (log.isDebugEnabled()) log.debug(e);
     474        if (log.isDebugEnabled()) log.debug("\t" + e);
    475475      }
    476476      catch (Exception e)
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/UnmappedPlateTransfer.java

    r3529 r3531  
    7070  {
    7171    super(userT, groupT);
     72    log.debug("Checking that necessary transfers have been done before proceeding with UnmappedPlate");
    7273    if (plateTypeT.isDone() && reporterT.isDone())
    7374    {
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/UploadFileTransfer.java

    r3529 r3531  
    103103  {
    104104    super(userT, groupT);
     105    log.debug("Checking that necessary transfers have been done before proceeding with UploadFile");
    105106    this.userfiles = path;
    106107    md5ToIdMap = new HashMap<String, Integer>();
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/UserTransfer.java

    r3529 r3531  
    9494  UserTransfer(RoleTransfer roleT, QuotaTransfer quotaT)
    9595  {
     96    log.debug("Checking that necessary transfers have been done before proceeding with User");
    9697    if (roleT.isDone() && quotaT.isDone())
    9798    {
     
    287288        dc.close();
    288289      }
    289       log.warn("FAILED when transfering user", e);
     290      log.warn("FAILED when transfering user");
     291      if (log.isDebugEnabled()) log.debug("\t" + e);
    290292    }
    291293    log.debug("--------------------------------------------------------------------------");
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/WellTransfer.java

    r3529 r3531  
    7676  public WellTransfer(UnmappedPlateTransfer unmappedPlateT)
    7777  {
     78    log.debug("Checking that necessary transfers have been done before proceeding with Well");
    7879    if (unmappedPlateT.isDone())
    7980    {
     
    215216    {
    216217      log.warn("Invalid data when annotate well");
    217       if (log.isDebugEnabled())log.debug(e);
     218      if (log.isDebugEnabled())log.debug("\t" + e);
    218219    }
    219220  }
  • trunk/src/clients/migrate/net/sf/basedb/clients/migrate/WizzzardTransfer.java

    r3529 r3531  
    103103      if (formatType != null && formatType.equals("result"))
    104104      {
    105         log.debug("Setting parameter values for a result-FormatType");
     105        log.debug("setting parameter value");
    106106        request.setParameterValue("rawDataType", "genepix");
    107107        PluginResponse response = request.invoke();
     
    315315    catch (BaseException e)
    316316    {
    317       log.warn("The transfer of wizzzard was interrupted");     
     317      log.warn("The transfer of wizzzard was interrupted");
     318      if (log.isDebugEnabled()) log.debug("\t" + e);
    318319    }
    319320    catch (SQLException e)
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